Computational Systems Biology
Sauro Lab
University of Washington
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Systems and Synthetic Biology

Start Date for Spring Term: January 5th

End Date for Spring Term: March 13th.

This page describes the systems and synthetic biology elective course, 498.

http://pbd.lbl.gov/sbconf/about.php


Course Description and Objectives Syllabus

This course offers an introduction to system and synthetic biology. This course is designed for seniors and/or graduates who have an interest in bioengineering at the cellular network level. Students will be introduced to the field of synthetic biology and its application in systems biology and applied engineering. Students will understand in quantitative terms the basic principles of operation of regulation at the cellular level, including metabolic, signaling and gene networks; discover how cellular networks can be reengineered, taking examples from the iGEM competitions and applications such as metabolic engineering; learn how to build computer models of cellular networks; appreciate that cellular systems are very noisy, particularly bacterial systems and how these can be modeled and studied experimentally. By the end of the course students will, by simple visual inspection of a network structure, will be able to make statements on the network’s possible dynamic behavior. This ability is a prerequisite for engineering new networks.

  1. Learn about biological parts and their properties. Understand gene and enzyme action.
  2. Learn about network structure and pathway engineering.
  3. Understand how synthetic networks can be simulated, built and tested in a real organism.
  4. Learn about manipulating DNA and measuring responses.
  5. Learn how to construct computational models and use them to study network behavior. Understand the behavior of basic network motifs found in cellular and synthetic systems, including switches, oscillators, filters, logic and pulse devices.
  6. Learn how to build complex modular networks in silico as part of a team project.

Basic course structure:

  1. Introduction of essential biological concepts
  2. Kinetics of Enzyme, Protein and Gene Regulation
  3. Network Structure, Molecular and Flux Conservation Laws
  4. Computational Methods (simulation)
  5. Basic Network Circuits
  6. Experimental Techniques in Molecular Biology
  7. Advanced Network Circuits - Bistability, Oscillators, Amplifiers, Filters and pulse generators.
  8. Team Project to design a complex network


Information on Jarnac

A note on the nature of models:

On Exactitude in Science

… In that Empire, the Art of Cartography attained such Perfection that the map of a single Province occupied the entirety of a City, and the map of the Empire, the entirety of a Province. In time, those Unconscionable Maps no longer satisfied, and the Cartographers Guilds struck a Map of the Empire whose size was that of the Empire, and which coincided point for point with it. The following Generations, who were not so fond of the Study of Cartography as their Forebears had been, saw that that vast Map was Useless, and not without some Pitilessness was it, that they delivered it up to the Inclemencies of Sun and Winters. In the Deserts of the West, still today, there are Tattered Ruins of that Map, inhabited by Animals and Beggars; in all the Land there is no other Relic of the Disciplines of Geography.

Suárez Miranda, Viajes de varones prudentes, Libro IV, Cap. XLV, Lérida, 1658

Borges, J. L. 1998. On exactitude in science. P. 325, In, Jorge Luis Borges, Collected Fictions (Trans. Hurley, H.) Penguin Books.


Power Point Slides:

Week 1: Introduction to Networks

PowerPoint 1

Non-stoichiometric Networks: Different Types

Introduction to Non-Stoichiometric Networks

Yeast two Hybrid and other Methods

Two review papers on p53 modification sites:

Post-translational modification of p53 in tumorigenesis

Regulating the p53 pathway: in vitro hypotheses, in vivo veritas

Assignment 1

Week 2:

Feedforward Networks

Complex Kinetics

Assignment 2

Week 3:

See last weeks slides for update

Bistable Systems

Assignment 3

Week 4

Genetic Logic Circuits

Oscillator Circuits

Read Parts and Devices

Sniffers Buzzers etc Paper + MODELS

Motif Review by Voigt

Week 5

Case Studies:

Assignment 4

Notes for Assignment 4

Stochastic Behavior

Stochastic Systems 1

Stochastic Systems 2

Notes on the Gillespie Algorithm

Assignment 5

Week 6

Stochastic Systems 3

Synthetic Biology and the Registry of Parts

BioBrick Standard Assembly

Week 7

In-Fusion BioBrick Assembly

Lab Scheduling Results

MidTerm Exam Topics:

1. Gene expression kinetics

2. Different kinds of network motifs: feedforwrd, bistable, oscillators, and combinations of.

3. Different kinds of parts, input and output devices.

4. Stochastic and deterministic systems.

5. Practical Assembly methods

Final Project Report Instructions

Last years computational projects:

  1. Biological Memory Storage and Routing
  2. Design and Functional Analysis of a New Carbon Fixation Pathway
  3. A Synthetic Biological Counter
  4. Design of a Low Glucose Induced Oscillator to Indicate Media Change
  5. The SwitchFrequency Oscillator
  6. Synthetic Chemotaxis Network
  7. Protein Network based Sawtooth Wave Generator

Lab Intro and Manuals

In-Fusion BioBrick Assembly and Re-engineering Lab Introduction (Version 2)

In-Fusion BioBrick Assembly and Re-engineering Lab Introduction (Version 2)

Laboratory 1 Manual (Version 2)

Laboratory 1 Manual (Version 2)

Lab Exercise 1

A Plasmid Editor (APE)

Laboratory 2 Manual (Version 2)

Laboratory 2 Manual (Version 2)

Laboratory 3 Manual

Laboratory 3 Manual

Fluorescence Microscopy Photos and Video

Week 7

Protein Networks

Week 8

Assignment 6

Week 9

Structural Analysis: Moiety Conservation

Solving Nonlinear Equations

Assignment 7

Week 10

Structural Analysis: Flux Relationships

Structural Analysis Application Version 2

Download zip file and unpack. Also download the 2008 redistributable binaries from Microsoft and install those, see link below:

Microsoft 2008 Redistributable

Start the application by double-clicking on Ambro.exe. See readme.txt, sample files and Doc.pdf for details.

Finals Assignment

Ignore all material from here on

Numerical Analysis Notes:

Solving Differential Equations

Assignment 2A

Assignment 2B

Brief Notes on Fitting Data to Functions

Test Data for Class Exercise

Test Data

Jarnac Notes

Control of Pathways

Review


The following documents are from last years course. See Syllabus for a description of the new syllabus.

Synthetic Biology Course Description 2007

Basic Syllabus

BioE 499 description

Link to 2007 web site:

499 Wiki, 2007

 
sysbio/labmembers/498_systems_and_synthetic_biology_winter_2009.txt · Last modified: 2009/11/13 15:13 (external edit)
 

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